David van der Spoel, can you please comment on this post of your from 2002:
"long timesteps combined with dummies give me unfolding proteins while without
dummies and 2 fs the systems are stable. These are long-time effects (i.e.
after a couple of ns things start to happen). I have to do more test
before I can conclude anything."
reference: http://www.gromacs.org/pipermail/gmx-users/2002-July/002171.html
I searched your name with the work timestep and looked through the
~200 titles of posts, but couldn't find anything.
I am currently considering a 5fs timestep and, even though it is
nicely described in the gromacs 4 paper, I wanted to ensure that
whatever problem you might have been experiencing is now solved.
Alternatively, if it was a particular type of system that appears to
be refractory to the 5fs timestep options (properly instituted with
dummies, etc) then that information would also be valuable to me.
My usage will be for free energy calculations of a protein in a lipid
bilayer so obtaining information on the dynamic processes is not
important to me here.
Thanks,
Chris.
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